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Current Genomics

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ISSN (Print): 1389-2029
ISSN (Online): 1875-5488

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Research Article

Identification of Plausible Candidates in Prostate Cancer Using Integrated Machine Learning Approaches

Author(s): Bhumandeep Kour, Nidhi Shukla, Harshita Bhargava, Devendra Sharma, Amita Sharma, Anjuvan Singh, Jayaraman Valadi, Trilok Chand Sadasukhi, Sugunakar Vuree* and Prashanth Suravajhala*

Volume 24, Issue 5, 2023

Published on: 21 November, 2023

Page: [287 - 306] Pages: 20

DOI: 10.2174/0113892029240239231109082805

Price: $65

Abstract

Background: Currently, prostate-specific antigen (PSA) is commonly used as a prostate cancer (PCa) biomarker. PSA is linked to some factors that frequently lead to erroneous positive results or even needless biopsies of elderly people.

Objectives: In this pilot study, we undermined the potential genes and mutations from several databases and checked whether or not any putative prognostic biomarkers are central to the annotation. The aim of the study was to develop a risk prediction model that could help in clinical decision-making.

Methods: An extensive literature review was conducted, and clinical parameters for related comorbidities, such as diabetes, obesity, as well as PCa, were collected. Such parameters were chosen with the understanding that variations in their threshold values could hasten the complicated process of carcinogenesis, more particularly PCa. The gathered data was converted to semi-binary data (-1, -0.5, 0, 0.5, and 1), on which machine learning (ML) methods were applied. First, we cross-checked various publicly available datasets, some published RNA-seq datasets, and our whole-exome sequencing data to find common role players in PCa, diabetes, and obesity. To narrow down their common interacting partners, interactome networks were analysed using GeneMANIA and visualised using Cytoscape, and later cBioportal was used (to compare expression level based on Z scored values) wherein various types of mutation w.r.t their expression and mRNA expression (RNA seq FPKM) plots are available. The GEPIA 2 tool was used to compare the expression of resulting similarities between the normal tissue and TCGA databases of PCa. Later, top-ranking genes were chosen to demonstrate striking clustering coefficients using the Cytoscape- cytoHubba module, and GEPIA 2 was applied again to ascertain survival plots.

Results: Comparing various publicly available datasets, it was found that BLM is a frequent player in all three diseases, whereas comparing publicly available datasets, GWAS datasets, and published sequencing findings, SPFTPC and PPIMB were found to be the most common. With the assistance of GeneMANIA, TMPO and FOXP1 were found as common interacting partners, and they were also seen participating with BLM.

Conclusion: A probabilistic machine learning model was achieved to identify key candidates between diabetes, obesity, and PCa. This, we believe, would herald precision scale modeling for easy prognosis.

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